Steady flow micro-reactor module for pipelined DNA computations

Abstract

Microflow reactors provide a means of implementing DNA Computing as a whole, not just individual steps. Contrary to surface based DNA Chips[1], microflow reactors with active components in closed flow systems can be used to integrate complete DNA computations[2]. Microreactors allow complicated flow topologies to be realized which can implement a dataflowlike architecture for the processing of DNA. A technologically feasible scalable approach with many reaction chambers however requires constant hydrodynamic flows. In this work, the experimental construction of a basic constant flow module for DNA processing in such a context is addressed. Limited diffusional exchange in parallel flows is used to establish spatio-temporal segregation of reaction conditions which can be crossed by magnetic beads without barriers. As previously outlined[2], linked up with an optical programming technology, this will enable DNA selection to be programmed and complex population selection to be performed. The basic first experimental step in the realization of this program is described here: the establishment of a stable hydrodynamic flow pattern which is scalable to many reactors in parallel and the demonstration of a scalable and synchronous clocking of magnetic beadbased processing. First results with fluorescently-labeled DNA transfer will also be presented at the conference. The way in which this module may be integrated to solve the maximal clique problem has been proposed elsewhere[2].